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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ), 'gf_id' => 'HOM05D001252', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001252' ), 'data_identifier' => 'HOM05D001252', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001252', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17520' => 'bna', 'A07p13030' => 'bna', 'A07p35700' => 'bna', 'A08p18520' => 'bna', 'A08p27440' => 'bna', 'A09p40040' => 'bna', 'Aa31LG1G1080' => 'aar', 'Aa31LG4G11460' => 'aar', 'Aa31LG7G8450' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3740' => 'aag', 'Actinidia10519' => 'ach', 'Actinidia10707' => 'ach', 'Actinidia12309' => 'ach', 'Actinidia23552' => 'ach', 'Actinidia33235' => 'ach', 'Actinidia38326' => 'ach', 'Ah.02g113840' => 'amhyb', 'Ah.10g035470' => 'amhyb', 'Ah.11g048150' => 'amhyb', 'AL1G25790' => 'aly', 'AL1G39100' => 'aly', 'AL2G28520' => 'aly', 'Aqoxy3G03522' => 'aox', 'Aqoxy5G02003' => 'aox', 'Aqoxy7G03421' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4Y4AAL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4ZSZ62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78JRYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV0606' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FVHL4G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GQA78F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TUP8NV' => 'arhy', 'AT1G13950' => 'ath', 'AT1G26630' => 'ath', 'AT1G69410' => 'ath', 'ATR0730G064' => 'atr', 'ATR0739G001' => 'atr', 'Atru.chr11.1704' => 'acertr', 'Atru.chr7.127' => 'acertr', 'AUR62005862' => 'cqu', 'AUR62005863' => 'cqu', 'AUR62005865' => 'cqu', 'AUR62032854' => 'cqu', 'AUR62032855' => 'cqu', 'AUR62032857' => 'cqu', 'BcaB03g12001' => 'bca', 'BcaB03g14079' => 'bca', 'BcaB03g15894' => 'bca', 'BcaB03g15902' => 'bca', 'BcaB05g24663' => 'bca', 'BcaB07g31721' => 'bca', 'BcaB07g31722' => 'bca', 'BcaB07g31723' => 'bca', 'BcaB08g34349' => 'bca', 'BcaC01g01752' => 'bca', 'BcaC04g22964' => 'bca', 'BcaC04g22965' => 'bca', 'BcaC05g26404' => 'bca', 'BcaC06g34120' => 'bca', 'BcaC06g35133' => 'bca', 'BolC3t19524H' => 'bol', 'BolC5t31172H' => 'bol', 'BolC6t39379H' => 'bol', 'BolC7t42467H' => 'bol', 'BolC7t43778H' => 'bol', 'BraA02t06798Z' => 'bra', 'BraA02t08419Z' => 'bra', 'BraA07t29074Z' => 'bra', 'BraA07t31158Z' => 'bra', 'BraA08t34685Z' => 'bra', 'BraA09t39500Z' => 'bra', 'C03p72290' => 'bna', 'C05p24380' => 'bna', 'C06p40520' => 'bna', 'C07p19480' => 'bna', 'C07p32470' => 'bna', 'CAN.G148.20' => 'can', 'CAN.G1512.1' => 'can', 'CAN.G160.68' => 'can', 'CAN.G216.3' => 'can', 'CAN.G460.1' => 'can', 'CAN.G479.52' => 'can', 'CAN.G491.1' => 'can', 'CAN.G551.41' => 'can', 'CAN.G59.19' => 'can', 'CAN.G66.9' => 'can', 'CAN.G912.9' => 'can', 'CANSAT11G0509' => 'cansat', 'CANSAT64G2390' => 'cansat', 'CARHR014320' => 'chi', 'CARHR025340' => 'chi', 'CARHR054370' => 'chi', 'CARHR062290' => 'chi', 'Carub.0001s2440' => 'cru', 'Carub.0002s1601' => 'cru', 'Carub.0006s0204' => 'cru', 'Ca_04894_v3' => 'car', 'Ca_13855_v3' => 'car', 'Ca_15744_v3' => 'car', 'Ca_21124_v3' => 'car', 'Ca_21728_v3' => 'car', 'Ca_21749_v3' => 'car', 'Ca_21801_v3' => 'car', 'Ca_30775_v3' => 'car', 'CBR_g4453' => 'cbr', 'Cc06_g15050' => 'ccan', 'Cc11_g12450' => 'ccan', 'CDE02G0343' => 'cde', 'CDE02G1886' => 'cde', 'CDE02G2362' => 'cde', 'CDE05G2912' => 'cde', 'CDE11G0102' => 'cde', 'Cfa008918' => 'cfa', 'Cfa019280' => 'cfa', 'Ciclev10009759m.g' => 'ccl', 'Ciclev10022624m.g' => 'ccl', 'Ciclev10032956m.g' => 'ccl', 'CiPaw.05G128900' => 'cil', 'CiPaw.11G048200' => 'cil', 'CiPaw.12G010500' => 'cil', 'CiPaw.15G177000' => 'cil', 'CiPaw.15G177700' => 'cil', 'CiPaw.15G178000' => 'cil', 'CiPaw.16G113200' => 'cil', 'ClCG05G016320' => 'cla', 'ClCG05G023950' => 'cla', 'ClCG06G012390' => 'cla', 'ClCG08G013700' => 'cla', 'COL.COLO4_18804' => 'col', 'COL.COLO4_27952' => 'col', 'COL.COLO4_27953' => 'col', 'Cpa.g.sc1.78' => 'cpa', 'Cpa.g.sc1348.1' => 'cpa', 'Cpa.g.sc1469.1' => 'cpa', 'Cre02.g097400' => 'cre', 'CsaV3_1G028950' => 'csa', 'CsaV3_2G032480' => 'csa', 'CsaV3_4G036580' => 'csa', 'CsaV3_5G033100' => 'csa', 'CSS0001122' => 'camsi', 'CSS0001971' => 'camsi', 'CSS0004833' => 'camsi', 'CSS0008498' => 'camsi', 'CSS0013383' => 'camsi', 'CSS0013887' => 'camsi', 'CSS0014850' => 'camsi', 'CSS0023470' => 'camsi', 'CSS0025080' => 'camsi', 'CSS0026902' => 'camsi', 'CSS0035689' => 'camsi', 'CSS0048543' => 'camsi', 'DCAR_014811' => 'dca', 'DCAR_017908' => 'dca', 'DCAR_026031' => 'dca', 'DCAR_030986' => 'dca', 'Dinv10666' => 'din', 'Dinv10669' => 'din', 'Dinv10673' => 'din', 'Dinv16696' => 'din', 'Dinv34105' => 'din', 'Dinv38755' => 'din', 'Dinv40972' => 'din', 'Dinv42860' => 'din', 'Dinv43240' => 'din', 'Duzib068G1293' => 'dzi', 'Duzib168G1395' => 'dzi', 'Duzib187G1984' => 'dzi', 'Duzib205G1861' => 'dzi', 'Duzib248G0022' => 'dzi', 'Duzib251G0601' => 'dzi', 'Duzib268G1661' => 'dzi', 'ECA233G0068' => 'eca', 'ECA240G2520' => 'eca', 'ECA240G4224' => 'eca', 'ECA246G0249' => 'eca', 'ECA246G2272' => 'eca', 'ECA246G2503' => 'eca', 'ECA246G5221' => 'eca', 'EL10Ac6g13279' => 'bvu', 'EL10Ac6g13281' => 'bvu', 'Eucgr.B00553' => 'egr', 'Eucgr.C00350' => 'egr', 'Eucgr.G02468' => 'egr', 'Eucgr.K02493' => 'egr', 'FAN04G2929' => 'fan', 'FAN11G1084' => 'fan', 'FAN12G1981' => 'fan', 'FAN12G2345' => 'fan', 'FAN12G2550' => 'fan', 'FAN13G0148' => 'fan', 'FAN16G1209' => 'fan', 'FAN17G2295' => 'fan', 'FAN18G0677' => 'fan', 'FAN21G0230' => 'fan', 'FAN22G0340' => 'fan', 'FAN23G1937' => 'fan', 'FAN24G1366' => 'fan', 'FAN26G1669' => 'fan', 'FAN28G0462' => 'fan', 'FvH4_1g00990' => 'fve', 'FvH4_4g30601' => 'fve', 'FvH4_4g34490' => 'fve', 'Glyma.01G054000' => 'gma', 'Glyma.02G112400' => 'gma', 'Glyma.02G203700' => 'gma', 'Glyma.04G165500' => 'gma', 'Glyma.05G024200' => 'gma', 'Glyma.06G197300' => 'gma', 'Glyma.17G103100' => 'gma', 'Glyma.18G192600' => 'gma', 'Gohir.A03G068000' => 'ghi', 'Gohir.A03G102900' => 'ghi', 'Gohir.A07G070000' => 'ghi', 'Gohir.A09G242900' => 'ghi', 'Gohir.A11G032600' => 'ghi', 'Gohir.A12G162900' => 'ghi', 'Gohir.A12G179900' => 'ghi', 'Gohir.D02G128100' => 'ghi', 'Gohir.D03G094500' => 'ghi', 'Gohir.D03G163950' => 'ghi', 'Gohir.D04G088916' => 'ghi', 'Gohir.D05G037550' => 'ghi', 'Gohir.D07G074600' => 'ghi', 'Gohir.D07G093866' => 'ghi', 'Gohir.D07G136750' => 'ghi', 'Gohir.D09G243600' => 'ghi', 'Gohir.D11G035900' => 'ghi', 'Gohir.D12G122933' => 'ghi', 'Gohir.D12G166000' => 'ghi', 'Gohir.D12G182600' => 'ghi', 'Gorai.001G078800' => 'gra', 'Gorai.003G098700' => 'gra', 'Gorai.004G130700' => 'gra', 'Gorai.005G024200' => 'gra', 'Gorai.005G143800' => 'gra', 'Gorai.006G267400' => 'gra', 'Gorai.007G038700' => 'gra', 'Gorai.008G178700' => 'gra', 'Gorai.008G195800' => 'gra', 'GSVIVG01003867001' => 'vvi', 'GSVIVG01007954001' => 'vvi', 'GSVIVG01035958001' => 'vvi', 'HanXRQChr08g0210561' => 'han', 'HanXRQChr08g0211051' => 'han', 'HanXRQChr09g0270931' => 'han', 'HanXRQChr12g0362701' => 'han', 'HanXRQChr15g0481631' => 'han', 'HanXRQChr15g0481651' => 'han', 'HanXRQChr15g0481661' => 'han', 'HanXRQChr16g0502561' => 'han', 'HanXRQChr16g0502611' => 'han', 'HanXRQChr16g0502761' => 'han', 'HanXRQChr17g0545401' => 'han', 'Haze_07661' => 'cav', 'Haze_11946' => 'cav', 'Haze_19211' => 'cav', 'Hma1.2p1_0028F.1_g017560' => 'hma', 'Hma1.2p1_0222F.1_g093510' => 'hma', 'Hma1.2p1_0354F.1_g133720' => 'hma', 'Hma1.2p1_0357F.1_g134350' => 'hma', 'HPP92_010148' => 'vpl', 'HPP92_012506' => 'vpl', 'HPP92_014241' => 'vpl', 'HPP92_015888' => 'vpl', 'HPP92_015896' => 'vpl', 'HPP92_016017' => 'vpl', 'HPP92_016037' => 'vpl', 'HPP92_018456' => 'vpl', 'HPP92_026502' => 'vpl', 'Hund02618' => 'sun', 'Hund03428' => 'sun', 'Hund06136' => 'sun', 'Hund09837' => 'sun', 'Hund19561' => 'sun', 'Hund25201' => 'sun', 'Lalb_Chr07g0178201' => 'lal', 'Lalb_Chr10g0098511' => 'lal', 'Lalb_Chr12g0197031' => 'lal', 'Lalb_Chr13g0303031' => 'lal', 'Lj1g0001765' => 'lja', 'Lj2A1063T76' => 'lonja', 'Lj2g0024435' => 'lja', 'Lj4g0016260' => 'lja', 'Lj4g0027088' => 'lja', 'Lj5C107T7' => 'lonja', 'Lj7A458G51' => 'lonja', 'Lj7C733T22' => 'lonja', 'Lj9C468G9' => 'lonja', 'Lj9C716T3' => 'lonja', 'Lsat_1_v5_gn_1_13341' => 'lsa', 'Lsat_1_v5_gn_3_116381' => 'lsa', 'Lsat_1_v5_gn_4_109761' => 'lsa', 'Lsat_1_v5_gn_5_21300' => 'lsa', 'Lsat_1_v5_gn_7_49720' => 'lsa', 'Lsat_1_v5_gn_7_82561' => 'lsa', 'Lsat_1_v5_gn_8_140460' => 'lsa', 'Lsat_1_v5_gn_8_46840' => 'lsa', 'Manes.05G107000' => 'mes', 'Manes.06G036000' => 'mes', 'Manes.06G088600' => 'mes', 'Manes.14G082350' => 'mes', 'Mapoly0045s0102' => 'mpo', 'MBI07_g39475_MAGBIO' => 'mbi', 'MBI14_g09682_MAGBIO' => 'mbi', 'MBI15_g19322_MAGBIO' => 'mbi', 'MBI19_g21017_MAGBIO' => 'mbi', 'MCO01G422' => 'mco', 'MCO03G383' => 'mco', 'MD02G1008000' => 'mdo', 'MD13G1067300' => 'mdo', 'MD15G1152300' => 'mdo', 'MD16G1066400' => 'mdo', 'Medtr3g437680' => 'mtr', 'Medtr4g109130' => 'mtr', 'Medtr4g112440' => 'mtr', 'Medtr4g130907' => 'mtr', 'Medtr4g130917' => 'mtr', 'Medtr5g042990' => 'mtr', 'MELO3C010222.2' => 'cme', 'MELO3C011298.2' => 'cme', 'MELO3C012131.2' => 'cme', 'MELO3C016963.2' => 'cme', 'Migut.E00065' => 'egut', 'Migut.J01338' => 'egut', 'Migut.L01232' => 'egut', 'MSTRG.10692' => 'ama', 'MSTRG.13437' => 'ama', 'MSTRG.19646' => 'ama', 'MSTRG.2326' => 'ama', 'MSTRG.26279' => 'ama', 'MSTRG.6134' => 'ama', 'MSTRG.7246' => 'ama', 'MSTRG.731' => 'ama', 'MSTRG.7771' => 'ama', 'Nitab4.5_0000014g0240' => 'nta', 'Nitab4.5_0000141g0010' => 'nta', 'Nitab4.5_0000720g0040' => 'nta', 'Nitab4.5_0001211g0130' => 'nta', 'Nitab4.5_0002315g0150' => 'nta', 'Nitab4.5_0002756g0020' => 'nta', 'Nitab4.5_0002891g0020' => 'nta', 'Nitab4.5_0008354g0040' => 'nta', 'Nitab4.5_0009049g0040' => 'nta', 'Nitab4.5_0011225g0040' => 'nta', 'Nn2g12356' => 'nnu', 'Nn3g17355' => 'nnu', 'Nn4g23305' => 'nnu', 'Nn8g39879' => 'nnu', 'Oeu016758.1' => 'oeu', 'Oeu021092.2' => 'oeu', 'Oeu024096.1' => 'oeu', 'Oeu026463.1' => 'oeu', 'Oeu031811.2' => 'oeu', 'Oeu046987.1' => 'oeu', 'Oeu055090.2' => 'oeu', 'Oeu057652.1' => 'oeu', 'Oeu057957.1' => 'oeu', 'Os03g0758800' => 'osa', 'Os07g0112800' => 'osa', 'Os07g0597000' => 'osa', 'Os12g0507200' => 'osa', 'Peaxi162Scf00062g00224' => 'pax', 'Peaxi162Scf00097g00108' => 'pax', 'Peaxi162Scf00187g01310' => 'pax', 'Peaxi162Scf00274g00004' => 'pax', 'Peaxi162Scf00401g00830' => 'pax', 'Peaxi162Scf01642g00002' => 'pax', 'PGR016G0007' => 'pgr', 'PGR044G0619' => 'pgr', 'PGR102G2771' => 'pgr', 'PGR119G1841' => 'pgr', 'PGR142G1847' => 'pgr', 'PGSC0003DMG400002819' => 'stu', 'PGSC0003DMG400007830' => 'stu', 'PGSC0003DMG400011137' => 'stu', 'PGSC0003DMG400024558' => 'stu', 'PGSC0003DMG400026829' => 'stu', 'Phvul.002G090900' => 'pvu', 'Phvul.003G156333' => 'pvu', 'Phvul.003G187500' => 'pvu', 'Phvul.009G184600' => 'pvu', 'Potri.006G185000' => 'ptr', 'Potri.008G092000' => 'ptr', 'Potri.010G162800' => 'ptr', 'Potri.018G107300' => 'ptr', 'Pp3c12_3540' => 'ppa', 'Pp3c13_15620' => 'ppa', 'PRCOL_00002691' => 'pco', 'Prupe.1G280900' => 'ppe', 'Prupe.7G262400' => 'ppe', 'Psat0s4638g0040' => 'psa', 'Psat2g127560' => 'psa', 'Psat4g044240' => 'psa', 'Psat4g109360' => 'psa', 'Psat5g201440' => 'psa', 'PSO017G2022' => 'pso', 'PSO478G4513' => 'pso', 'QL02p093167' => 'qlo', 'QL03p069981' => 'qlo', 'QL03p070000' => 'qlo', 'QL03p070009' => 'qlo', 'QL10p017993' => 'qlo', 'QL10p018036' => 'qlo', 'RcHm_v2.0_Chr2g0085721' => 'rch', 'RcHm_v2.0_Chr4g0439011' => 'rch', 'Rhsim02G0213300' => 'rsi', 'Rhsim03G0257000' => 'rsi', 'Rhsim12G0133400' => 'rsi', 'Sabra06G0140500' => 'sbr', 'Sabra08G0068900' => 'sbr', 'Sabra10G0123800' => 'sbr', 'Sabra18G0091300' => 'sbr', 'SalBow1G2486' => 'sbo', 'SalBow8G4493' => 'sbo', 'Sc04g0002930' => 'sci', 'Sc04g0007800' => 'sci', 'Sc10g0009800' => 'sci', 'Sc14g0008060' => 'sci', 'Sc23g0006390' => 'sci', 'Sed0008566' => 'sed', 'Sed0012692' => 'sed', 'Sed0018573' => 'sed', 'Sed0018846' => 'sed', 'Sed0024537' => 'sed', 'SEGI_06317' => 'sgi', 'SEGI_17117' => 'sgi', 'SGA_v2.0_scaffold130G34303' => 'sas', 'SGA_v2.0_scaffold16G07744' => 'sas', 'SGA_v2.0_scaffold265G46108' => 'sas', 'SGA_v2.0_scaffold265G46109' => 'sas', 'SGA_v2.0_scaffold313G48318' => 'sas', 'SGA_v2.0_scaffold36G14414' => 'sas', 'SGA_v2.0_scaffold45G17035' => 'sas', 'SGA_v2.0_scaffold63G21637' => 'sas', 'SMO356G0352' => 'smo', 'Solyc01g011000.3' => 'sly', 'Solyc03g115650.4' => 'sly', 'Solyc04g005510.3' => 'sly', 'Solyc05g006890.1' => 'sly', 'Solyc07g005560.3' => 'sly', 'Solyc12g010060.2' => 'sly', 'Sopen01g006960' => 'spe', 'Sopen03g034640' => 'spe', 'Sopen04g001530' => 'spe', 'Sopen07g001660' => 'spe', 'Sopen12g004940' => 'spe', 'Sp1g12310' => 'spa', 'Sp1g22170' => 'spa', 'Sp3g30940' => 'spa', 'Sp5g24460' => 'spa', 'TAR371G1062' => 'tar', 'TAR374G0702' => 'tar', 'TAR383G0110' => 'tar', 'TAR622G0349' => 'tar', 'TAR626G1501' => 'tar', 'THA.LOC104799766' => 'tha', 'THA.LOC104801813' => 'tha', 'THA.LOC104805181' => 'tha', 'THA.LOC104808630' => 'tha', 'THA.LOC104822030' => 'tha', 'THA.LOC104822903' => 'tha', 'THA.LOC104824069' => 'tha', 'Thecc.02G338400' => 'tca', 'Thecc.03G095100' => 'tca', 'Thecc.09G031300' => 'tca', 'Thhalv10008974m.g' => 'esa', 'Thhalv10008978m.g' => 'esa', 'Thhalv10019263m.g' => 'esa', 'Thhalv10027391m.g' => 'esa', 'Thhalv10029433m.g' => 'esa', 'TPR.G12278' => 'tpr', 'TPR.G19942' => 'tpr', 'TPR.G2035' => 'tpr', 'TPR.G24880' => 'tpr', 'TPR.G25641' => 'tpr', 'TPR.G2821' => 'tpr', 'TWI15G0948' => 'twi', 'TWI34G1203' => 'twi', 'TWI60G1438' => 'twi', 'TWI63G1671' => 'twi', 'TWI79G0038' => 'twi', 'TWI81G0512' => 'twi', 'unitig_22.g5553' => 'ugi', 'unitig_8.g3962' => 'ugi', 'vmacro06084' => 'vma', 'vmacro11244' => 'vma', 'vmacro16356' => 'vma', 'VMungo1215G1119' => 'vmu', 'VMungo1215G2219' => 'vmu', 'VMungo1215G2751' => 'vmu', 'VMungo1309G0208' => 'vmu', 'Zm00001eb017820' => 'zma', 'Zm00001eb108410' => 'zma', 'Zm00001eb118210' => 'zma', 'Zm00001eb148180' => 'zma', 'Zm00001eb218360' => 'zma', 'Zm00001eb326630' => 'zma', 'Zm00001eb373470' => 'zma' ) $gf_id = 'HOM05D001252' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001252' ) $data_identifier = 'HOM05D001252' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 4, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 9, 'sun' => (int) 6, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 9, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 5, 'pso' => (int) 2, 'qlo' => (int) 6, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 8, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb373470' $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